polySegratioMM (version 0.6-2)

setInits: Set up and dump initial values given the model and prior

Description

Given a model of class modelSegratioMM and priors of class priorsSegratioMM, initial values are computed using approximate expected values by setInits and then written to file by dumpInits

Usage

setInits(model, priors, seed = 1)
dumpInits(inits, stem = "test", inits.file = paste(stem, "-inits.R",
  sep = ""))

Arguments

model

Object of class modelSegratioMM providing model attributes like the number of components and ploidy level

priors

Object of class priorsSegratioMM

seed

Seed to be used for JAGS runs. If a number of chains are to be run a vector of starting values may be specified. However, see note below.

inits

A list of initial values usually produced by setInits

stem

File name stem for inits file (default test)

inits.file

Inits file name which is automatically generated from stem if not specified

Value

• Returns a list with the following initial values:
• mu
  Mean of dosage classes on logit scale: usually c(0,NA,NA,...,NA)
• P
  Initial value for proportion in each dosage class
• tau
  Precision of means which depends on whether priors are strong or weak
• theta
  Differences in means (for parameterisation employed for better convergence)
• seed
  Sets seed for each MCMC chain (Default:1)
• taub
  If the model contains a random effect then sets initial value of precision of random effect b which is normally distributed with mean 0 and precision taub

concept

• segregation ratio
• dominant marker
• autopolyploid

See Also

setModel setPriors setControl dumpInits

Examples

## simulate small autooctaploid data set
a1 <- sim.autoMarkers(8,c(0.7,0.2,0.1),n.markers=100,n.individuals=50)

## set up model, priors, inits etc and write files for JAGS
x <- setModel(3,8)
x2 <- setPriors(x)
inits <- setInits(x,x2)
dumpInits(inits)